Begin by downloading observations from iNaturalist. Use this link: https://www.inaturalist.org/observations/export. For this demonstration, I specified only observations from North America and entered “Danaus plexippus” in the “Taxon” search field. Besides that, I left all of the default options. This dataset contains about 50,000 observations and took about 10 minutes to compile and download. Once it’s ready, you will be directed to a link that has a zipped folder which contains a .csv file that has all of the data. The .csv file should have a name like “observations-59866.csv”.
Establish directory (put the downloaded .csv file here; all outputs will also go here)
knitr::opts_knit$set(root.dir = '../monarch_map_gif/')
Load necessary libraries; if you don’t have these installed yet, you’ll have to do that first using install.packages(‘name_of_package’)
library(ggplot2); library(plyr); library(rnaturalearth); library(gganimate); library(gapminder); library(gifski)
Load the data and take a look. This could take a little while, depending on the size of the file.
inat.monarchs <- read.csv(file = './observations-59866.csv')
head(inat.monarchs)
## id observed_on_string observed_on time_observed_at
## 1 1813 2009-03-01 2009-03-01
## 2 3340 2009-09-13 2009-09-13
## 3 6171 2009-06-08 2009-06-08
## 4 8128 2010-08-28 2010-08-28
## 5 13261 2009-06-09 2009-06-09
## 6 14880 November 18, 2010 2010-11-18
## time_zone out_of_range user_id user_login
## 1 Eastern Time (US & Canada) 169 flapack
## 2 Eastern Time (US & Canada) 169 flapack
## 3 Pacific Time (US & Canada) 382 tsoleau
## 4 Eastern Time (US & Canada) 19 justinscioli
## 5 Pacific Time (US & Canada) 714 curiousgeorge61
## 6 Eastern Time (US & Canada) 1000 muir
## created_at updated_at quality_grade license
## 1 2009-03-03 05:32:59 UTC 2019-01-31 01:37:29 UTC research CC-BY-NC
## 2 2009-09-19 01:43:13 UTC 2018-03-26 19:35:46 UTC research CC-BY-NC
## 3 2010-03-23 05:46:37 UTC 2017-12-13 21:04:44 UTC research
## 4 2010-08-29 19:31:35 UTC 2017-12-13 21:05:11 UTC research
## 5 2011-03-24 20:49:20 UTC 2017-12-13 21:06:16 UTC research CC-BY-NC
## 6 2011-04-20 00:43:42 UTC 2017-12-13 21:06:38 UTC research CC-BY-NC
## url
## 1 http://www.inaturalist.org/observations/1813
## 2 http://www.inaturalist.org/observations/3340
## 3 http://www.inaturalist.org/observations/6171
## 4 http://www.inaturalist.org/observations/8128
## 5 http://www.inaturalist.org/observations/13261
## 6 http://www.inaturalist.org/observations/14880
## image_url
## 1 https://static.inaturalist.org/photos/2182/medium.jpg?1444937202
## 2 https://static.inaturalist.org/photos/5295/medium.jpg?1444497296
## 3 https://static.inaturalist.org/photos/12387/medium.jpg?1444282344
## 4 https://static.inaturalist.org/photos/18079/medium.jpg?1444294036
## 5 https://static.inaturalist.org/photos/26215/medium.JPG
## 6 https://static.inaturalist.org/photos/28970/medium.JPG
## sound_url tag_list
## 1 NA
## 2 NA
## 3 NA
## 4 NA Monarch, danaus plexippus, butterfly
## 5 NA June, butterfly
## 6 NA
## description
## 1
## 2
## 3
## 4 Tons of butterflies were everywhere in Eastern Pennsylvania. This monarch was at the edge of a corn field where some milkweed was growing.
## 5
## 6
## id_please num_identification_agreements num_identification_disagreements
## 1 false 4 0
## 2 false 3 0
## 3 false 2 0
## 4 false 3 0
## 5 false 2 0
## 6 false 2 0
## captive_cultivated oauth_application_id place_guess latitude
## 1 false NA Pine Island Ridge, FL 26.07879
## 2 false NA Pine Island Ridge, FL 26.08047
## 3 false NA Cambria, CA 35.55769
## 4 false NA Adamstown, PA 40.24120
## 5 false NA Pepperwood Preserve, CA 38.56666
## 6 false NA Santa Cruz, CA 36.95401
## longitude positional_accuracy geoprivacy taxon_geoprivacy
## 1 -80.27837 NA
## 2 -80.27792 NA
## 3 -121.08159 NA
## 4 -76.05633 NA
## 5 -122.68481 NA
## 6 -122.02724 NA
## coordinates_obscured positioning_method positioning_device species_guess
## 1 false Monarch
## 2 false Monarch
## 3 false Monarque
## 4 false Monarque
## 5 false Monarque
## 6 false Monarque
## scientific_name common_name iconic_taxon_name taxon_id
## 1 Danaus plexippus Monarch Insecta 48662
## 2 Danaus plexippus Monarch Insecta 48662
## 3 Danaus plexippus Monarch Insecta 48662
## 4 Danaus plexippus Monarch Insecta 48662
## 5 Danaus plexippus Monarch Insecta 48662
## 6 Danaus plexippus Monarch Insecta 48662
names(inat.monarchs)
## [1] "id" "observed_on_string"
## [3] "observed_on" "time_observed_at"
## [5] "time_zone" "out_of_range"
## [7] "user_id" "user_login"
## [9] "created_at" "updated_at"
## [11] "quality_grade" "license"
## [13] "url" "image_url"
## [15] "sound_url" "tag_list"
## [17] "description" "id_please"
## [19] "num_identification_agreements" "num_identification_disagreements"
## [21] "captive_cultivated" "oauth_application_id"
## [23] "place_guess" "latitude"
## [25] "longitude" "positional_accuracy"
## [27] "geoprivacy" "taxon_geoprivacy"
## [29] "coordinates_obscured" "positioning_method"
## [31] "positioning_device" "species_guess"
## [33] "scientific_name" "common_name"
## [35] "iconic_taxon_name" "taxon_id"
Filter out captive reared and non-research-grade observations.
inat.monarchs <- inat.monarchs[inat.monarchs$captive_cultivated=='false',]
inat.monarchs <- inat.monarchs[inat.monarchs$quality_grade == 'research',]
Pick which columns to keep
columns.keep <- c('id','observed_on','quality_grade','place_guess','latitude','longitude','url')
inat.monarchs <- inat.monarchs[,columns.keep]
Specify observations to exclude. These are some observations that, despite being research grade, are not relevant, such as dead monarchs found in melted snow. I’ve almost certainly missed a few; this list can be updated.
urls.exclude <- c('https://www.inaturalist.org/observations/9373451','https://www.inaturalist.org/observations/20483568','https://www.inaturalist.org/observations/9879408','https://www.inaturalist.org/observations/20320860','https://www.inaturalist.org/observations/21799902','https://www.inaturalist.org/observations/19494799','https://www.inaturalist.org/observations/11410855','https://www.inaturalist.org/observations/5740325','https://www.inaturalist.org/observations/7469853','https://www.inaturalist.org/observations/18866685','https://www.inaturalist.org/observations/18357363','https://www.inaturalist.org/observations/19379295')
inat.monarchs <- inat.monarchs[-(inat.monarchs$url %in% urls.exclude),] #exclude the above observations
Plot observations onto a world map. Note: observations here are only from North America, since that is what I specified when I downloaded the data from iNaturalist.
world <- ne_countries(scale= 'medium',returnclass = 'sf') #retrieve map layer (uses rnaturalearth package)
ggplot(data = world)+
geom_sf()+
theme_bw()+
geom_point(data = inat.monarchs, aes(x = longitude, y = latitude), size = 0.5, col = 'blue')+
theme(legend.position = 'none')+
theme(axis.title = element_blank())
Okay, now it’s time to make the actual .gif itself.
First, we need to define a static plot that contains all of the data.
(plot.static <- ggplot(data = world)+
geom_sf()+
theme_bw()+
theme(axis.title = element_blank(), axis.text = element_blank())+
xlim(c(-130,-60))+
ylim(c(12,60))+
theme(legend.position = 'none')+
geom_point(data = inat.monarchs,
aes(x = longitude, y = latitude, col = julian.date), size = 1)+
scale_color_viridis_c())
## Warning: Removed 93 rows containing missing values (geom_point).
Now use this map template to generate an animated .gif
Arguments and what they do:
transition_time() specifies what to use for indexing / what order to put plots in
shadow_wake() will leave a “trail” or “imprint” behind after each point appears, with the time that it remains visible defined by the wake_length argument
shadow_mark() will leave a permanent mark after a point appear.
monarchs.anim <- plot.static + transition_time(julian.date) +
shadow_wake(wake_length = 0.5, alpha = FALSE)+
shadow_mark(alpha = 0.4, size = 0.6)
Display the .gif!!!
monarchs.anim
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